Gene Expression Profile of Pulpitis
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Downregulation of Salivary Proteins, Protective Against Dental Caries, in Type 1 Diabetes
proteomes Article Downregulation of Salivary Proteins, Protective against Dental Caries, in Type 1 Diabetes Eftychia Pappa 1,* , Konstantinos Vougas 2, Jerome Zoidakis 2 , William Papaioannou 3, Christos Rahiotis 1 and Heleni Vastardis 4 1 Department of Operative Dentistry, School of Dentistry, National and Kapodistrian University of Athens, 11527 Athens, Greece; [email protected] 2 Proteomics Laboratory, Biomedical Research Foundation Academy of Athens, 11527 Athens, Greece; [email protected] (K.V.); [email protected] (J.Z.) 3 Department of Preventive and Community Dentistry, School of Dentistry, National and Kapodistrian University of Athens, 11527 Athens, Greece; [email protected] 4 Department of Orthodontics, School of Dentistry, National and Kapodistrian University of Athens, 11527 Athens, Greece; [email protected] * Correspondence: effi[email protected] Abstract: Saliva, an essential oral secretion involved in protecting the oral cavity’s hard and soft tissues, is readily available and straightforward to collect. Recent studies have analyzed the sali- vary proteome in children and adolescents with extensive carious lesions to identify diagnostic and prognostic biomarkers. The current study aimed to investigate saliva’s diagnostic ability through proteomics to detect the potential differential expression of proteins specific for the occurrence of carious lesions. For this study, we performed bioinformatics and functional analysis of proteomic datasets, previously examined by our group, from samples of adolescents with regulated and unreg- ulated type 1 diabetes, as they compare with healthy controls. Among the differentially expressed Citation: Pappa, E.; Vougas, K.; proteins relevant to caries pathology, alpha-amylase 2B, beta-defensin 4A, BPI fold containing family Zoidakis, J.; Papaioannou, W.; Rahiotis, C.; Vastardis, H. -
Human Identification by Amelogenin Test in Libyans
American Journal of www.biomedgrid.com Biomedical Science & Research ISSN: 2642-1747 --------------------------------------------------------------------------------------------------------------------------------- Research Article Copyright@ Samir Elmrghni Human Identification by Amelogenin Test in Libyans Samir Elmrghni* and Mahmoud Kaddura Department of Forensic Medicine and Toxicology, University of Benghazi, Libya *Corresponding author: Samir Elmrghni, Faculty of Medicine, Department of Forensic Medicine and Toxicology, University of Benghazi-Libya, Benghazi, Libya. To Cite This Article: Samir Elmrghni. Human Identification by Amelogenin Test in Libyans. Am J Biomed Sci & Res. 2019 - 3(6). AJBSR. MS.ID.000737. DOI: 10.34297/AJBSR.2019.03.000737 Received: May 25, 2019 | Published: July 11, 2019 Abstract Sex typing is essential in medical diagnosis of sex-linked disease and forensic science. Gender for criminal evidence of offender is usually as reported the anomalous amelogenin results of 2 male samples (out of 238 males) represented as females (Y deletions) and another 2 samples the initial information for investigation. For individualization, identification of gender is performed in addition to the STR markers recently. We amelogenin results of the controversial samples, DNA was further used in SRY and Y-STR typing. All samples typed as males but two showed with with (X deletions) in Benghazi (Libya). The frequency in both was about 0.8%. Higher than those of the other populations reported. To confirm X chromosomes. From the results, it was highly suggested that for the controversial cases of human gender identification with amelogenin tests, amplificationKeywords: Amelogenin; of SRY gene Libyans or/and Y-STR markers will be adopted to confirm the gender [1]. Introduction gene (AMG) was precisely mapped in the p22 region on the X systems used to determine if the sample being tested is of male gene was first isolated and sequenced [2]. -
Tooth Enamel and Its Dynamic Protein Matrix
International Journal of Molecular Sciences Review Tooth Enamel and Its Dynamic Protein Matrix Ana Gil-Bona 1,2,* and Felicitas B. Bidlack 1,2,* 1 The Forsyth Institute, Cambridge, MA 02142, USA 2 Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA * Correspondence: [email protected] (A.G.-B.); [email protected] (F.B.B.) Received: 26 May 2020; Accepted: 20 June 2020; Published: 23 June 2020 Abstract: Tooth enamel is the outer covering of tooth crowns, the hardest material in the mammalian body, yet fracture resistant. The extremely high content of 95 wt% calcium phosphate in healthy adult teeth is achieved through mineralization of a proteinaceous matrix that changes in abundance and composition. Enamel-specific proteins and proteases are known to be critical for proper enamel formation. Recent proteomics analyses revealed many other proteins with their roles in enamel formation yet to be unraveled. Although the exact protein composition of healthy tooth enamel is still unknown, it is apparent that compromised enamel deviates in amount and composition of its organic material. Why these differences affect both the mineralization process before tooth eruption and the properties of erupted teeth will become apparent as proteomics protocols are adjusted to the variability between species, tooth size, sample size and ephemeral organic content of forming teeth. This review summarizes the current knowledge and published proteomics data of healthy and diseased tooth enamel, including advancements in forensic applications and disease models in animals. A summary and discussion of the status quo highlights how recent proteomics findings advance our understating of the complexity and temporal changes of extracellular matrix composition during tooth enamel formation. -
Amelogenin Gene Influence on Enamel Defects of Cleft Lip and Palate Patients
ORIGINAL RESEARCH Genetic and Molecular Biology Amelogenin gene influence on enamel defects of cleft lip and palate patients Abstract: The aim of this study was to investigate the occurrence of mutations in the amelogenin gene (AMELX) in patients with cleft lip Fernanda Veronese OLIVEIRA(a) Thiago José DIONÍSIO(b) and palate (CLP) and enamel defects (ED). A total of 165 patients were Lucimara Teixeira NEVES(b) divided into four groups: with CLP and ED (n=46), with CLP and with- Maria Aparecida Andrade out ED (n = 34), without CLP and with ED (n = 34), and without CLP Moreira MACHADO(a) Carlos Ferreira SANTOS(b) or ED (n = 51). Genomic DNA was extracted from saliva followed by Thais Marchini OLIVEIRA(a) conducting a Polymerase Chain Reaction and direct DNA sequencing of exons 2 through 7 of AMELX. Mutations were found in 30% (n = 14), (a) Department of Pediatric Dentistry, 35% (n = 12), 11% (n = 4) and 13% (n = 7) of the subjects from groups 1, 2, Orthodontics and Community Health, Bauru 3 and 4, respectively. Thirty seven mutations were detected and distrib- School of Dentistry, University of São Paulo, Bauru, SP, Brazil. uted throughout exons 2 (1 mutation – 2.7%), 6 (30 mutations – 81.08%) and 7 (6 mutations – 16.22%) of AMELX. No mutations were found in (b) Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, exons 3, 4 or 5. Of the 30 mutations found in exon 6, 43.34% (n = 13), Bauru, SP, Brazil. 23.33% (n = 7), 13.33% (n = 4) and 20% (n = 6) were found in groups 1, 2, 3 and 4, respectively. -
X-Linked Diseases: Susceptible Females
REVIEW ARTICLE X-linked diseases: susceptible females Barbara R. Migeon, MD 1 The role of X-inactivation is often ignored as a prime cause of sex data include reasons why women are often protected from the differences in disease. Yet, the way males and females express their deleterious variants carried on their X chromosome, and the factors X-linked genes has a major role in the dissimilar phenotypes that that render women susceptible in some instances. underlie many rare and common disorders, such as intellectual deficiency, epilepsy, congenital abnormalities, and diseases of the Genetics in Medicine (2020) 22:1156–1174; https://doi.org/10.1038/s41436- heart, blood, skin, muscle, and bones. Summarized here are many 020-0779-4 examples of the different presentations in males and females. Other INTRODUCTION SEX DIFFERENCES ARE DUE TO X-INACTIVATION Sex differences in human disease are usually attributed to The sex differences in the effect of X-linked pathologic variants sex specific life experiences, and sex hormones that is due to our method of X chromosome dosage compensation, influence the function of susceptible genes throughout the called X-inactivation;9 humans and most placental mammals – genome.1 5 Such factors do account for some dissimilarities. compensate for the sex difference in number of X chromosomes However, a major cause of sex-determined expression of (that is, XX females versus XY males) by transcribing only one disease has to do with differences in how males and females of the two female X chromosomes. X-inactivation silences all X transcribe their gene-rich human X chromosomes, which is chromosomes but one; therefore, both males and females have a often underappreciated as a cause of sex differences in single active X.10,11 disease.6 Males are the usual ones affected by X-linked For 46 XY males, that X is the only one they have; it always pathogenic variants.6 Females are biologically superior; a comes from their mother, as fathers contribute their Y female usually has no disease, or much less severe disease chromosome. -
Amelogenin X Linked Chromosome
International Journal of Research in Medical Sciences Gupta B. Int J Res Med Sci. 2017 Oct;5(10):4214-4222 www.msjonline.org pISSN 2320-6071 | eISSN 2320-6012 DOI: http://dx.doi.org/10.18203/2320-6012.ijrms20174549 Review Article Amelogenin x linked chromosome Bhawani Gupta* Department of Oral Pathology, Saveetha University, Chennai, Tamil Nadu, India Received: 29 June 2017 Revised: 20 August 2017 Accepted: 21 August 2017 *Correspondence: Dr. Bhawani Gupta, E-mail: [email protected] Copyright: © the author(s), publisher and licensee Medip Academy. This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT The AMELX gene provides instructions for making a protein called amelogenin, which is essential for normal tooth development. Amelogenin is involved in the formation of enamel, which is the hard, white material that forms the protective outer layer of each tooth. Using molecular genetic techniques, we have shown that there is no evidence that the AMGX gene is deleted in this case of the Nance-Horan syndrome. In affected members of a Michigan kindred of Eastern European ancestry segregating X-linked amelogenesis imperfecta with a characteristic snow-capped enamel phenotype. Keywords: Amelogenin, Chromosome, Hormone INTRODUCTION degradation by Proteolytic enzymes like matrix mettaloproteinases into smaller low molecular weight The AMELX gene provides instructions for making a fragments, like tyrosine rich amelogenin protein and protein called amelogenin, which is essential for normal leucine rich amelogenin polypeptide which are suggested tooth development. -
Analysis of 5000 Year-Old Human Teeth Using Optimized Large-Scale And
Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, Clément Zanolli, Rémi Esclassan, Richard Donat, Catherine Thèves, Odile Burlet-Schiltz, et al. To cite this version: Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, et al.. Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides. Journal of Proteomics, Elsevier, 2020, 211, pp.103548. 10.1016/j.jprot.2019.103548. hal-02322441 HAL Id: hal-02322441 https://hal.archives-ouvertes.fr/hal-02322441 Submitted on 18 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Journal Pre-proof Analysis of 5000year-old human teeth using optimized large- scale and targeted proteomics approaches for detection of sex- specific peptides Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, Clément Zanolli, Rémi Esclassan, Richard Donat, Catherine Thèves, Odile Burlet- Schiltz, Catherine Mollereau PII: S1874-3919(19)30320-3 DOI: https://doi.org/10.1016/j.jprot.2019.103548 Reference: JPROT 103548 To appear in: Journal of Proteomics Received date: 24 January 2019 Revised date: 30 August 2019 Accepted date: 7 October 2019 Please cite this article as: C. -
Establishing Gene Amelogenin As Sex-Specific Marker in Yak By
Journal of Genetics (2019) 98:7 © Indian Academy of Sciences https://doi.org/10.1007/s12041-019-1061-x RESEARCH NOTE Establishing gene Amelogenin as sex-specific marker in yak by genomic approach P. P. DA S 1,G.KRISHNAN2, J. DOLEY1, D. BHATTACHARYA3,S.M.DEB4, P. CHAKRAVARTY1 and P. J. DAS5∗ 1Indian Council of Agricultural Research-National Research Centre on Yak, Dirang 790 101, India 2Indian Council of Agricultural Research -National Institute of Animal Nutrition and Physiology, Bengaluru 560 030, India 3Indian Council of Agricultural Research -Central Island Agricultural Research Institute, Garacharama, Port Blair 744 101, India 4Indian Council of Agricultural Research -National Dairy Research Institute, Karnal 132 001, India 5Indian Council of Agricultural Research-National Research Centre on Pig, Rani, Guwahati 781 131, India *For correspondence. E-mail: [email protected], [email protected]. Received 20 June 2018; revised 3 October 2018; accepted 6 October 2018; published online 12 February 2019 Abstract. Yak, an economically important bovine species considered as lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. Amelogenin is an essential protein for tooth enamel which eutherian mammals contain two copies in both X and Y chromosome each. In bovine, the deletion of a fragment of the nucleotide sequence in Y chromosome copy of exon 6 made Amelogenin an excellent sex-specific marker.Thus,anattemptwasmadetousethegeneasanadvancedmolecularmarkerofsexingoftheyaktoimprovebreeding strategies and reproduction. The present study confirmed that the polymerase chain reaction amplification of the Amelogenin gene with a unique primer is useful in sex identification of the yak. -
Genome-Wide Expression Profiling Establishes Novel Modulatory Roles
Batra et al. BMC Genomics (2017) 18:252 DOI 10.1186/s12864-017-3635-4 RESEARCHARTICLE Open Access Genome-wide expression profiling establishes novel modulatory roles of vitamin C in THP-1 human monocytic cell line Sakshi Dhingra Batra, Malobi Nandi, Kriti Sikri and Jaya Sivaswami Tyagi* Abstract Background: Vitamin C (vit C) is an essential dietary nutrient, which is a potent antioxidant, a free radical scavenger and functions as a cofactor in many enzymatic reactions. Vit C is also considered to enhance the immune effector function of macrophages, which are regarded to be the first line of defence in response to any pathogen. The THP- 1 cell line is widely used for studying macrophage functions and for analyzing host cell-pathogen interactions. Results: We performed a genome-wide temporal gene expression and functional enrichment analysis of THP-1 cells treated with 100 μM of vit C, a physiologically relevant concentration of the vitamin. Modulatory effects of vitamin C on THP-1 cells were revealed by differential expression of genes starting from 8 h onwards. The number of differentially expressed genes peaked at the earliest time-point i.e. 8 h followed by temporal decline till 96 h. Further, functional enrichment analysis based on statistically stringent criteria revealed a gamut of functional responses, namely, ‘Regulation of gene expression’, ‘Signal transduction’, ‘Cell cycle’, ‘Immune system process’, ‘cAMP metabolic process’, ‘Cholesterol transport’ and ‘Ion homeostasis’. A comparative analysis of vit C-mediated modulation of gene expression data in THP-1cells and human skin fibroblasts disclosed an overlap in certain functional processes such as ‘Regulation of transcription’, ‘Cell cycle’ and ‘Extracellular matrix organization’, and THP-1 specific responses, namely, ‘Regulation of gene expression’ and ‘Ion homeostasis’. -
DEFA3 Rabbit Pab
Leader in Biomolecular Solutions for Life Science DEFA3 Rabbit pAb Catalog No.: A5340 Basic Information Background Catalog No. Defensins are a family of antimicrobial and cytotoxic peptides thought to be involved in A5340 host defense. They are abundant in the granules of neutrophils and also found in the epithelia of mucosal surfaces such as those of the intestine, respiratory tract, urinary Observed MW tract, and vagina. Members of the defensin family are highly similar in protein sequence 13kDa and distinguished by a conserved cysteine motif. The protein encoded by this gene, defensin, alpha 3, is found in the microbicidal granules of neutrophils and likely plays a Calculated MW role in phagocyte-mediated host defense. Several alpha defensin genes are clustered 10kDa on chromosome 8. This gene differs from defensin, alpha 1 by only one amino acid. This gene and the gene encoding defensin, alpha 1 are both subject to copy number Category variation. Primary antibody Applications WB Cross-Reactivity Human Recommended Dilutions Immunogen Information WB 1:500 - 1:2000 Gene ID Swiss Prot 1668 P59666 Immunogen Recombinant fusion protein containing a sequence corresponding to amino acids 20-94 of human DEFA3 (NP_005208.1). Synonyms DEFA3;DEF3;HNP-3;HNP3;HP-3;HP3 Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts of various cell lines, using DEFA3 antibody (A5340) at 1:1000 dilution. Secondary antibody: HRP Goat Anti-Rabbit IgG (H+L) (AS014) at 1:10000 dilution. -
Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis
Getting “Under the Skin”: Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis by Kristen Monét Brown A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Epidemiological Science) in the University of Michigan 2017 Doctoral Committee: Professor Ana V. Diez-Roux, Co-Chair, Drexel University Professor Sharon R. Kardia, Co-Chair Professor Bhramar Mukherjee Assistant Professor Belinda Needham Assistant Professor Jennifer A. Smith © Kristen Monét Brown, 2017 [email protected] ORCID iD: 0000-0002-9955-0568 Dedication I dedicate this dissertation to my grandmother, Gertrude Delores Hampton. Nanny, no one wanted to see me become “Dr. Brown” more than you. I know that you are standing over the bannister of heaven smiling and beaming with pride. I love you more than my words could ever fully express. ii Acknowledgements First, I give honor to God, who is the head of my life. Truly, without Him, none of this would be possible. Countless times throughout this doctoral journey I have relied my favorite scripture, “And we know that all things work together for good, to them that love God, to them who are called according to His purpose (Romans 8:28).” Secondly, I acknowledge my parents, James and Marilyn Brown. From an early age, you two instilled in me the value of education and have been my biggest cheerleaders throughout my entire life. I thank you for your unconditional love, encouragement, sacrifices, and support. I would not be here today without you. I truly thank God that out of the all of the people in the world that He could have chosen to be my parents, that He chose the two of you. -
A Machine Learning Pipeline for Discriminant Pathways Identification
A MACHINE LEARNING PIPELINE FOR DISCRIMINANT PATHWAYS IDENTIFICATION Annalisa Barla(1), Giuseppe Jurman(2), Roberto Visintainer(2;3) Margherita Squillario(1), Michele Filosi(2;4), Samantha Riccadonna(2) and Cesare Furlanello(2) 1DISI, University of Genoa, via Dodecaneso 35, I-16146 Genova, Italy. 2FBK, via Sommarive 18, I-38123 Povo (Trento), Italy. 3DISI, University of Trento, via Sommarive 14, I-38123 Povo (Trento), Italy. 4CIBIO, University of Trento, via Delle Regole 101, I-38123 Mattarello (Trento), Italy CONTENTS 1 Introduction 1 2 System and Methods 2 3 Data Description 3 3.1 Children susceptibility to air pollution 3 3.2 Clinical stages of Parkinson’s disease 3 3.3 Clinical stages of Alzheimer’s disease 3 4 Discussion 3 4.1 Air Pollution Experiment 3 4.2 Parkinson’s Disease Experiment 4 4.3 Alzheimer’s Disease Experiment 7 5 Conclusion 9 6 Appendix 10 6.1 Experimental setup for the examples 10 6.1.1 Spectral Regression Discriminant Analysis (SRDA). 10 6.1.2 The `1`2 feature selection framework (`1`2FS ). 10 6.1.3 Functional Characterization. 10 6.1.4 Weighted Gene Co-Expression Networks (WGCN). 10 6.1.5 Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE). 10 6.1.6 Ipsen-Mikhailov distance . 10 6.2 Experiments 11 6.2.1 Air Pollution Experiment 11 6.2.2 Parkinson’s Disease Experiment 13 6.2.3 Alzheimer’s Disease Experiment 17 arXiv:1105.4486v2 [q-bio.MN] 27 May 2011 ABSTRACT Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology.